Bootstrap-based support of HGT inferred by maximum parsimony

BMC Evolutionary Biology

Volumn 10, Issue 1, 2010, Pages

  Park, Hyun Jung ^a   Jin, Guohua ^a   Nakhleh, Luay ^a  

^a Rice University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DATA SET; GENE TRANSFER; PARSIMONY ANALYSIS; PHYLOGENETICS; RECONSTRUCTION; SOFTWARE;

ARTICLE; BIOLOGICAL MODEL; COMPUTER PROGRAM; GENETICS; HORIZONTAL GENE TRANSFER; PHYLOGENY; PLANT;

GENE TRANSFER, HORIZONTAL; MODELS, GENETIC; PHYLOGENY; PLANTS; SOFTWARE;

EID: 77951800222     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-10-131     Document Type: Article

References (27)

1. Phylogenetic networks. B Gemeinholzer, Analysis of Biological Networks John Wiley and Sons Ltd, Junker BH, Schreiber F, 2008 255 282
2. Split networks and Reticulate Networks. D Huson, Reconstructing Evolution, New Mathematical and Computational Advances Oxford University Press, Gascuel O, Steel M, 2007 247 276
3. Application of Phylogenetic Networks in Evolutionary Studies. D Huson D Bryant, Molecular Biology and Evolution 2006 23 2 254 267 10.1093/molbev/msj030 16221896
4. Network (Reticulate) Evolution: Biology, Models, and Algorithms. C Linder BE Moret L Nakhleh T Warnow, The Pacific Symposium on Biocomputing 2004
5. Phylogenetic Network Construction Approaches. V Makarenkov D Kevorkov P Legendre, Applied Mycology and Biotechnology 2006 61 97
6. Networks in phylogenetic analysis: new tools for population biology. D Morrison, International Journal of Parasitology 2005 35 567 582 10.1016/j.ijpara.2005.02.007 15826648
7. Evolutionary Phylogenetic Networks: Models and Issues. L Nakhleh, The Problem Solving Handbook for Computational Biology and Bioinformatics Springer, Heath L, Ramakrishnan N, 2010 [To appear].
8. Toward defining the course of evolution: Minimum change for a specified tree topology. W Fitch, Syst Zool 1971 20 406 416 10.2307/2412116
9. Computationally difficult parsimony problems in phylogenetic systematics. W Day, Journal of Theoretical Biology 1983 103 429 438 10.1016/0022-5193(83) 90296-5
10. The Steiner Problem in Phylogeny is NP-complete. L Foulds R Graham, Adv Appl Math 1982 3 43 49 10.1016/S0196-8858(82)80004-3
11. PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods). D Swofford, Sinauer Associates, Underland, Massachusetts, Version 4.0 1966
12. Reconstructing evolution of sequences subject to recombination using parsimony. J Hein, Math Biosciences 1990 98 185 200 10.1016/0025-5564(90)90123-G (Pubitemid 20171457)
13. A heuristic method to reconstruct the history of sequences subject to recombination. J Hein, J Mol Evol 1993 36 396 405 10.1007/BF00182187
14. Reconstructing phylogenetic networks using maximum parsimony. L Nakhleh G Jin F Zhao J Mellor-Crummey, Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB2005) 2005 93 102
15. Inferring phylogenetic networks by the maximum parsimony criterion: A case study. G Jin L Nakhleh S Snir T Tuller, Molecular Biology and Evolution 2007 24 324 337 10.1093/molbev/msl163 17068107
16. Efficient parsimony-based methods for phylogenetic network reconstruction. G Jin L Nakhleh S Snir T Tuller, Bioinformatics [Proceedings of the European Conference on Computational Biology (ECCB 06)] 2006 23 123 e128
17. A New Linear-time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. G Jin L Nakhleh S Snir T Tuller, Proceedings of the International Symposium on Bioinformatics Research and Applications Lecture Notes in Bioinformatics, Mandoiu I, Zelikovsky A, 2007 4463 61 72
18. Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-time Heuristic. G Jin L Nakhleh S Snir T Tuller, IEEE/ACM Transactions on Computational Biology and Bioinformatics 2009 6 3 495 505 10.1109/TCBB.2008.119
19. Inferring and validating horizontal gene transfer events using bipartition dissimilarity. A Boc H Philippe V Makarenkov, Systematic Biology 2010 59 195 211 10.1093/sysbio/syp103
20. Phylogenetic networks: Modeling, reconstructibility, and accuracy. B Moret L Nakhleh T Warnow C Linder A Tholse A Padolina J Sun R Timme, IEEE/ACM Transactions on Computational Biology and Bioinformatics 2004 1 13 23 10.1109/TCBB.2004.10
21. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to basal angiosperm Amborella. U Bergthorsson A Richardson G Young L Goertzen J Palmer, Proc Nat'l Acad Sci USA 2004 101 17747 17752 10.1073/pnas.0408336102 (Pubitemid 40051958)
22. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic. D Hillis J Bull, Systematic Biology 1993 42 182 192
23. Applying the bootstrap in phylogeny reconstruction. P Soltis D Soltis, Statistical Science 2003 18 256 267 10.1214/ss/1063994980 (Pubitemid 37545098)
24. PhyloGen: Phylogenetic tree simulator package. A Rambaut, 2002 http://tree.bio.ed.ac.uk/software/phylogen/
25. A model of horizontal gene transfer and the bacterial phylogeny problem. N Galtier, Systematic Biology 2007 56 4 633 642 10.1080/10635150701546231 17661231
26. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. H Shimodaira M Hasegawa, Molecular Biology and Evolution 1999 16 1114 1116
27. Maximum likelihood of phylogenetic networks. G Jin L Nakhleh S Snir T Tuller, Bioinformatics 2006 22 21 2604 2611 10.1093/bioinformatics/btl452 16928736